title: Prosecutor: parameter-free inference of gene function for prokaryotes using DNA microarray data, genomic context and multiple gene annotation sources.
abstract: BACKGROUND
  Despite a plethora of functional genomic efforts, the function of many genes in sequenced genomes remains unknown. The increasing amount of microarray data for many species allows employing the guilt-by-association principle to predict function on a large scale: genes exhibiting similar expression patterns are more likely to participate in shared biological processes.
  
  
  RESULTS
  We developed Prosecutor, an application that enables researchers to rapidly infer gene function based on available gene expression data and functional annotations. Our parameter-free functional prediction method uses a sensitive algorithm to achieve a high association rate of linking genes with unknown function to annotated genes. Furthermore, Prosecutor utilizes additional biological information such as genomic context and known regulatory mechanisms that are specific for prokaryotes. We analyzed publicly available transcriptome data sets and used literature sources to validate putative functions suggested by Prosecutor. We supply the complete results of our analysis for 11 prokaryotic organisms on a dedicated website.
  
  
  CONCLUSIONS
  The Prosecutor software and supplementary datasets available at http://www.prosecutor.nl allow researchers working on any of the analyzed organisms to quickly identify the putative functions of their genes of interest. A de novo analysis allows new organisms to be studied.
authors.affiliation: Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, the Netherlands. e.j.blom@rug.nl
authors.forename: Evert Jan
authors.initials: EJ
authors.lastname: Blom
authors.forename: Rainer
authors.initials: R
authors.lastname: Breitling
authors.forename: Klaas Jan
authors.initials: KJ
authors.lastname: Hofstede
authors.forename: Jos B T M
authors.initials: JB
authors.lastname: Roerdink
authors.forename: Sacha A F T
authors.initials: SA
authors.lastname: van Hijum
authors.forename: Oscar P
authors.initials: OP
authors.lastname: Kuipers
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods; D004926:Escherichia coli / Q000235:genetics; D005786:Gene Expression Regulation; D023281:Genomics; D020411:Oligonucleotide Array Sequence Analysis; D012441:Saccharomyces cerevisiae / Q000235:genetics; D017422:Sequence Analysis, DNA; D012984:Software; D014158:Transcription, Genetic